Time-resolved fluorescence analysis of the mobile flavin cofactor in p -hydroxybenzoate hydroxylase

Conformational heterogeneity of the FAD cofactor in p-hydroxybenzoate hydroxylase (PHBH) was investigated with time-resolved polarized flavin fluorescence. For binary enzyme/substrate (analogue) complexes of wild-type PHBH and Tyr222 mutants, crystallographic studies have revealed two distinct flavin conformations; the ‘in’ conformation with the isoalloxazine ring located in the active site, and the ‘out’ conformation with the isoalloxazine ring disposed towards the protein surface. Fluorescence-lifetime analysis of these complexes revealed similar lifetime distributions for the ‘in’ and ‘out’ conformations. The reason for this is twofold. First, the active site of PHBH contains various potential fluorescence-quenching sites close to the flavin. Fluorescence analysis of uncomplexed PHBH Y222V and Y222A showed that Tyr222 is responsible for picosecond fluorescence quenching free enzyme. In addition, other potential quenching sites, including a tryptophan and two tyrosines involved in substrate binding, are located nearby. Since the shortest distance between these quenching sites and the isoalloxazine ring differs only little on average, these aromatic residues are likely to contribute to fluorescence quenching. Second, the effect of flavin conformation on the fluorescence lifetime distribution is blurred by binding of the aromatic substrates: saturation with aromatic substrates induces highly efficient fluorescence quenching. The flavin conformation is therefore only reflected in the small relative contributions of the longer lifetimes.     

Solid-State NMR Study of Phase Separation and Order of Water Molecules and Silanol Groups in Polysiloxane Networks

Homogeneity and structure of organically modified polysiloxane networks prepared by sol-gel co-condensation, as well as location and nature of water molecules and silanol groups were studied by 1D and 2D solid-state NMR. ¹H–²⁹Si and ¹H–¹H interatomic distances were estimated from variable contact-time CP/MAS experiments, ¹H NMR chemical shifts and off-resonance WISE NMR. A structure model of these networks is proposed and discussed. The fraction of proton-inaccessible units Q⁴ in the networks decreases with increasing amounts of dimethylsiloxane (D) and methylsiloxane (T) units. In contrast to systems prepared by co-condensation of tetraethoxysilane (TEOS) with dimethyl(diethoxy)silane (DMDEOS), proton-inaccessible units form essential fraction in networks prepared by co-condensation of TEOS with methyl(triethoxy)silane (MTEOS). The proton-accessible part of the networks with high O/Si ratios is nano-heterogeneous phase, which is composed of water containing Q ⁱ particles separated by copolymer domains. The overall homogeneity and uniformity of binding sites around silanol groups increases by co-condensation TEOS with DMDEOS or MTEOS, while the amount of physisorbed water as well as the hydrogen bond strength decreases, as compared with neat silica gel prepared by polycondensation of TEOS.     

Preparation and characterization of dendrimer-star PNIPAAM using dithiobenzoate-terminated PPI dendrimer via RAFT polymerization

Two dendritic reversible addition-fragmentation transfer (RAFT) agents with 8 and 16 terminal dithiobenzoate (DTB) groups on the surface of poly(propylene imine) (PPI) dendrimers (generation 2.0 and 3.0, respectively) were successively prepared, and they were used in the RAFT polymerization of N-isopropylacrylamide (NIPAAM). The polymerization kinetics was confirmed to pseudo-first-order behavior. The ¹H NMR and GPC analyses show that the dendrimer-star den (NIPAAM)_x (x = 8 or 16) prepared by RAFT method has well-defined structure, controlled molecular weight and low polydispersities (PDI < 1.3). The aqueous solution prepared from dendrimer-star PNIPAAM showed reversible changes in optical properties: transparent below a lower critical solution temperature (LCST) and opaque above the LCST.     

Electron Transfer and Charge Transfer: Twin Themes in Unifying the Mechanisms of Organic and Organometallic Reactions

The broad varieties of organic and organometallic reactions merge into a common unifying mechanism by considering all nucleophiles and electrophiles as electron donors (D) and electron acceptors (A), respectively. Comparison of outer-sphere and inner-sphere electron transfers with the aid of Marcus theory provides the thermochemical basis for the generalized free energy relationship for electron transfer (FERET) in Equation (37) and its corollaries in Equations (43) and (44) that have wide predictive applicability to electrophilic aromatic substitutions, olefin additions, organometallic cleavages, etc. The FERET is based on the conversion of the weak nucleophile–electrophile interactions extant in the ubiquitous electron donor—acceptor (EDA) precursor complex [D, A] to the radical ion pair [D^⊕, A^?], for which the free energy change can be evaluated from the charge-transfer absorption spectra according to Mulliken theory. FERET analysis thus indicates that the charge-transfer ion pairs [D^⊕, A^?] are energetically equivalent to the transition states for nucleophile/electrophile transformations. The behavior of such ion pairs can be directly observed immediately following the irradiation of the charge-transfer bands of various EDA complexes with a 25-ps laser pulse. Such studies confirm the radical ion pair [Arene^⊕, NO₂] as a viable intermediate in electrophilic aromatic nitration, as presented in the electron-transfer mechanism between arenes and the nitryl cation (NO) electrophile.     

Spectroscopic and Quantum Mechanical Studies of Substituted Anilines and their Charge-Transfer Complexes with Iodine in Different Solvents

Summary. Equilibrium constants and molar extinction coefficients for 1:1 charge-transfer complexes between 2-hydroxyaniline (HA), 5-chloro-2-hydroxyaniline (CHA), and 4-bromo-2,6-dimethylaniline (BMA) as donors and iodine, as a typical σ-acceptor were determined spectrophotometrically in chloroform, dichloromethane, and carbontetrachloride solutions. Spectral characteristics and formation constants are discussed in terms of donor molecular structure and solvent polarity. The stoichiometry of the complexes was established to be 1:1. For this purpose, optical data were subjected to the form of the Rose-Drago equation for 1:1 equilibria. Electronic absorption spectra of the studied anilines were measured in different solvents. Spectral data were reported and band maxima were assigned to the appropriate molecular orbital transitions (π–π^* and n–π^* electronic transition). Solvent effects on the electronic transitions were discussed. Optimized geometry of the studied anilines was obtained at B3LYP/6-31 + G(d). The effect of the electronic factors of the substituents on the geometrical parameters of the ring has been explored. Geometrical values of the ring deviate from the regular hexagonal ring. Intramolecular H-bonds in HA and CHA have been computed at B3LYP/6-31 + G(d) and MP2/6-31 + G(d) levels. The H-bonding distance was calculated to be 2.105 ? in HA and 2.127 ? in CHA. Abstracted from her M.Sc. thesis     

三重四极杆电感耦合等离子体质谱(ICP-MS)法测定氧化铕中13种稀土杂质元素

稀土杂质元素直接影响高纯单金属稀土材料的整体性能,是高科技领域许多材料的重要组成部分。通过考察最佳的消解酸量、温度、时间、氧气反应气流量、稀释气流量,建立了基于三重四极杆电感耦合等离子体质谱仪(ICP-MS/MS)直接测定氧化铕中13种稀土杂质元素分析方法。该方法采用0.1%基体直接进样,可以很大程度提高前处理分析效率。利用碰撞模式测定氧化铕稀土中的Y、La、Pr、Nd、Sm、Gd、Tb、Dy、Ho、Er、Yb、Lu元素,氧气质量转移模式测定氧化铕中的Tm,两种模式结合可以有效去除多原子干扰,实现氧化铕的稳定测试分析。通过对氧化铕标准物质（GBW02902）直接测定分析,结果表明,在碰撞和氧气质量转移模式下,各元素线性相关系数（r）均大于 0.9999,方法检出限为0.001~0.023 mg/kg,测试精密度优于1.99%,13种元素的测试值都在认定值的不确定度范围之内。该分析方法操作简单,测试稳定,效率高,为实验室进行氧化铕材料中REE杂质的准确测试分析提供思路和借鉴。     

Domain Adaptation with Data Uncertainty Measure Based on Evidence Theory

Domain adaptation aims to learn a classifier for a target domain task by using related labeled data from the source domain. Because source domain data and target domain task may be mismatched, there is an uncertainty of source domain data with respect to the target domain task. Ignoring the uncertainty may lead to models with unreliable and suboptimal classification results for the target domain task. However, most previous works focus on reducing the gap in data distribution between the source and target domains. They do not consider the uncertainty of source domain data about the target domain task and cannot apply the uncertainty to learn an adaptive classifier. Aimed at this problem, we revisit the domain adaptation from source domain data uncertainty based on evidence theory and thereby devise an adaptive classifier with the uncertainty measure. Based on evidence theory, we first design an evidence net to estimate the uncertainty of source domain data about the target domain task. Second, we design a general loss function with the uncertainty measure for the adaptive classifier and extend the loss function to support vector machine. Finally, numerical experiments on simulation datasets and real-world applications are given to comprehensively demonstrate the effectiveness of the adaptive classifier with the uncertainty measure.     

Sensing the ortho Positions in C6Cl6 and C6H4Cl2 from Cl2− Formation upon Molecular Reduction

The geometrical effect of chlorine atom positions in polyatomic molecules after capturing a low-energy electron is shown to be a prevalent mechanism yielding Cl₂⁻. In this work, we investigated hexachlorobenzene reduction in electron transfer experiments to determine the role of chlorine atom positions around the aromatic ring, and compared our results with those using ortho-, meta- and para-dichlorobenzene molecules. This was achieved by combining gas-phase experiments to determine the reaction threshold by means of mass spectrometry together with quantum chemical calculations. We also observed that Cl₂⁻ formation can only occur in 1,2-C₆H₄Cl₂, where the two closest C–Cl bonds are cleaved while the chlorine atoms are brought together within the ring framework due to excess energy dissipation. These results show that a strong coupling between electronic and C–Cl bending motion is responsible for a positional isomeric effect, where molecular recognition is a determining factor in chlorine anion formation.     

一例含阴离子水簇的钴配合物的合成、结构及理论研究

金属配合物中的水簇研究为研究宏观意义上的水以及与蛋白质分子有关的水分子提供了有效途径。本文合成了一个含有阴离子水簇的带状超分子配合物[Co(2,2-bipy)₂(N₃)₂](N₃)_0.5Cl_0.5·2H₂O(1,2, 2-bipy=2, 2-联吡啶)。单晶结构解析表明,配合物属于三斜晶系,P-1空间群,晶胞参数为:a=0.822 54(7) nm,b=1.175 58(9) nm,c=1.237 06(10) nm,α=91.379 0(10)°,β=92.151 0(10)°,γ=108.119 0(10)°,V=1.135 27(16) nm³,由一个单核[Co(2,2-bipy)₂(N₃)₂]⁺配合物阳离子、两个非配位水分子、0.5个游离的叠氮离子和0.5个氯离子组成,叠氮离子和氯离子位置无序,占有率各为50%。两个客体水分子通过强烈的分子间氢键作用形成了环状水四聚体,且与无序的N^-₃和Cl^-通过氢键作用形成了一个[(H₂O)₄(N₃)Cl]^2- 阴离子水簇。此外,本文基于密度泛函理论(DFT)对配合物[Co(2,2-bipy)₂(N₃)₂]⁺阳离子进行了量子化学计算,分析了其单点能和原子电荷,并计算了中心金属离子的氧化态,计算结果与实验相吻合。     

Precise Quantification of Molybdate In Vitro by the FRET-Based Nanosensor ‘MolyProbe’

Molybdenum (Mo) is an essential trace element in all kingdoms of life. Mo is bioavailable as the oxyanion molybdate and gains biological activity in eukaryotes when bound to molybdopterin, forming the molybdenum cofactor. The imbalance of molybdate homeostasis results in growth deficiencies or toxic symptoms within plants, fungi and animals. Recently, fluorescence resonance energy transfer (FRET) methods have emerged, monitoring cellular and subcellular molybdate distribution dynamics using a genetically encoded molybdate-specific FRET nanosensor, named MolyProbe. Here, we show that the MolyProbe system is a fast and reliable in vitro assay for quantitative molybdate determination. We added a Strep-TagII affinity tag to the MolyProbe protein for quick and easy purification. This MolyProbe is highly stable, resistant to freezing and can be stored for several weeks at 4 °C. Furthermore, the molybdate sensitivity of the assay peaked at low nM levels. Additionally, The MolyProbe was applied in vitro for quantitative molybdate determination in cell extracts of the plant Arabidopsis thaliana, the fungus Neurospora crassa and the yeast Saccharomyces cerevisiae. Our results show the functionality of the Arabidopsis thaliana molybdate transporter MOT1.1 and indicate that FRET-based molybdate detection is an excellent tool for measuring bioavailable Mo.